WebGrabber

Annotation and TF-fingerprint files are currently supplied with Expander for yeast, human, mouse, rat, fly, zebrafish, c-elegans and chicken. Annotation files are supplied also for E. coli and Listeria. These files are updated on a regular basis.

The following conventional gene Ids are used in the annotation and TF-fingerprint files:

Organism	ID type
Human	Entrez / Locus Link
Mouse	Entrez / Locus Link
Rat	Entrez / Locus Link
Yeast	ORF codes
Fly	FlyBase
c-elegans	WormBase
Arabidopsis	AGI Ids
Zebrafish	Ensembl
Chicken	Ensembl
E. coli*	Uniprot
Listeria*	Entrez / Locus Link
S. pombe	Entrez / Locus Link

The gene ontology and annotation files supplied with Expander are based on data that was downloaded from the GO website.

The following table specifies the database from which these files are derived for each of the organisms that we support, and the date of download from GO site:

Organism	Extracted from	Updated on
Human	GOA@EBI	May 2007
Mouse	MGI (Mouse Genome Informatics)	May 2007
Rat	GOA@EBI	October 2007
Yeast	SGD (Saccharomyces Genome Database)	October 2007
Fly	FlyBase	January 2005
c-elegans	WormBase	October 2007
Arabidopsis	TAIR (The Arabidopsis information resource)	October 2007
Zebrafish	ZFIN	May 2007
Chicken	GOA@EBI	January 2008
e.coli	EBI	April 2008
Listeria	Blast2Go	February 2009
S. pombe	NCBI	November 2008

The following TF fingerprint files (and sequence files) can be downloaded from our web download page (as part of the zip supplied for each organism).

Organism	Promoter sequences range	Promoter sequences origin	TF Models origin
Human	3000 bp upstream the TSS to 200 bp downstream the TSS.	Ensembl release 42	TRANSFAC (version 8.2)
Mouse	3000 bp upstream the TSS to 200 bp downstream the TSS.	Ensembl release 42	TRANSFAC (version 8.2)
Rat	3000 bp upstream the TSS to 200 bp downstream the TSS.	Ensembl release 47	TRANSFAC (version 8.2)
Yeast	600 bp upstream CDS to CDS	SGD January 2007	TRANSFAC (version 8.2) & Harbison et al. 2004 (see References)
Fly	3000 bp upstream the TSS to 200 bp downstream the TSS.	Ensembl release 43	TRANSFAC (version 8.2)
C-elegans	3000 bp upstream the TSS to 200 bp downstream the TSS.	Ensembl release 44	TRANSFAC (version 8.2)
Arabidopsis	1000 bp upstream the TSS to 200 bp downstream the TSS.	TAIR: The Arabidopsis Information Resource (December '06)	TRANSFAC (version 8.2)
Zebrafish	3000 bp upstream the TSS to 200 bp downstream the TSS.	Ensembl release 44	TRANSFAC (version 8.2)
Chicken	3000 bp upstream the TSS to 200 bp downstream the TSS.	Ensembl release 43	TRANSFAC (version 8.2)
S. pombe	600 bp upstream CDS to CDS	Sanger gene DB October 2008	TRANSFAC (version 8.2) & Harbison et al. 2004

The following miRNA target scan files can be downloaded from our web download page (as part of the zip supplied for each organism).

Organism	Extracted from	Updated on
Human	TargetScan website	TargetScan5
Mouse	TargetScan website	TargetScan5
Fly	TargetScan website	TargetScan5
c-elegans	TargetScan website	TargetScan5

The following gene position files can be downloaded from our web download page (as part of the zip supplied for each organism). It is used to display the gene chromosomal positions.

Organism	Extracted from	Updated on
Human	UCSC genome browser	January 2009
Mouse	UCSC genome browser	January 2009
Rat	UCSC genome browser	January 2009
Fly	UCSC genome browser	January 2009
c-elegans	UCSC genome browser	January 2009
Zebrafish	UCSC genome browser	January 2009

Gene ID conversion files for many of the Affymetrix chips can be downloaded from the Expander download page. The files map each Affymetrix Id into the corresponding gene Id. Conversion files are generated and added to the download page according to user requests. If you can't find the file you need here, please look it up in the download page, and contact us if it's not there.

Organism	Chip name
Human	HG-Focus
Human	HGU1332
Human	HG-U95E
Human	HG-U133A
Human	HT_HG-U133A
Human	HG-U133Plus2
Human	Hu-35KsubB
Human	HuGene-1_0-ST
Mouse	MGU74Av2
Mouse	MGU430_2
Mouse	MG430A2
Mouse	MoGene-1_0-ST
Rat	RGU34A
Rat	Rat230_2
Rat	Agilent
C-elegans	C. elegans Genome Chip
Arabidopsis	ATH1
Zebra-Fish	GeneChip Zebrafish Genome Array
Chicken	Affymetrix Chicken Genome Chip
E. coli	Affymetrix E. coli Antisense Genome Array
E. coli	Affymetrix E. coli Genome 2.0 Array

Organism	File name	Network origin
Human	Expander.hsa.RualNature05.sif	Towards a proteome-scale map of the human protein-protein interaction network by Rual JF et al. Nature. 437(7062):1173-8 (2005)
Human	Expander.hsa.IntAct.sif	IntAct database (http://www.ebi.ac.uk/intact/)
Mouse	Expander.mmu.IntAct.sif	IntAct database (http://www.ebi.ac.uk/intact/)
Rat	Expander.rno.IntAct.sif	IntAct database (http://www.ebi.ac.uk/intact/)
Worm	Expander.cel.SimonisNatMethods08.sif	Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network by Simonis N. et al. Nature Methods 6, 47 - 54 (2009)
Fly	Expander.dme.DroID.sif	DroID database (http://www.droidb.org/)
Yeast	Expander.sce.United.sif	1. High-Quality Binary Protein Interaction Map of the Yeast Interactome Network by Yu et al. Science 322(5898):104 � 110 (2008) 2. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae by Reguly et al. Journal of Biology 5(4):11 (2006) 3. Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae by Collins SR et al. Molecular Cell Proteomics 6(3):439-50 (2007)
Arabidopsis	Expander.ath.TAIR.sif	TAIR database (http://www.arabidopsis.org/)
E. coli	Expander.eco.Arifuzzaman06.txt	Large-scale identification of protein�protein interaction of Escherichia coli K-12 by Arifuzzaman M et al. Genome Research 16(5):686-91. (2006)

Supplied Files

Network origin